On 4/15/13 3:01 AM, fatemeh ramezani wrote:
Dear Justin
I thought by use of -pairs I can calculate energy between any 2 groups from
index file. when I use g_energy, result is a .xvg file that shows energy of
system but I need to calculate energy between specific groups. is there any way
for me?
That is not what -pairs does, per the help description. If you want the energy
of different components of the system (i.e. residues), you need to set
appropriate energygrps in the .mdp file such that short-range nonbonded terms
are decomposed. If you did not do this in your simulation, create a new .tpr
file with appropriate groups and re-calculate the energies using the original
trajectory with mdrun -rerun. Doing so does not decompose long-range terms
(i.e. PME).
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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